gtexr (version 0.2.1)

get_variant: Get Variant

Description

This service returns information about a variant, including position, dbSNP RS ID, the reference allele, the alternative allele, and whether the minor allele frequency is >= 1%. For GTEx v6p, there is also information about whether the whole exome sequence and chip sequencing data are available. Results may be queried by GTEx variant ID (variantId), dbSNP RS ID (snpId) or genomic location (chromosome and pos). Variants are identified based on the genotype data of each dataset cohort, namely, are dataset-dependent. Each variant is assigned a unique GTEx variant ID (i.e. the primary key). Not all variants have a mappable dbSNP RS ID. By default, this service queries the latest GTEx release.

GTEx Portal API documentation

Usage

get_variant(
  snpId = NULL,
  variantId = NULL,
  datasetId = "gtex_v8",
  chromosome = NULL,
  poss = NULL,
  page = 0,
  itemsPerPage = getOption("gtexr.itemsPerPage"),
  .verbose = getOption("gtexr.verbose"),
  .return_raw = FALSE
)

Value

A tibble. Or a list if .return_raw = TRUE.

Arguments

snpId

String

variantId

String. A gtex variant ID.

datasetId

String. Unique identifier of a dataset. Usually includes a data source and data release. Options: "gtex_v8", "gtex_snrnaseq_pilot".

chromosome

String. One of "chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr7", "chr8", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chr22", "chrM", "chrX", "chrY".

poss

Integer, vector.

page

Integer (default = 0).

itemsPerPage

Integer (default = 250). Set globally to maximum value 100000 with options(list(gtexr.itemsPerPage = 100000)).

.verbose

Logical. If TRUE (default), print paging information. Set to FALSE globally with options(list(gtexr.verbose = FALSE)).

.return_raw

Logical. If TRUE, return the raw API JSON response. Default = FALSE

See Also

Other Datasets Endpoints: get_annotation(), get_collapsed_gene_model_exon(), get_downloads_page_data(), get_file_list(), get_full_get_collapsed_gene_model_exon(), get_functional_annotation(), get_linkage_disequilibrium_by_variant_data(), get_linkage_disequilibrium_data(), get_sample_datasets(), get_subject(), get_tissue_site_detail(), get_variant_by_location()

Examples

if (FALSE) { # identical(Sys.getenv("IN_PKGDOWN"), "true")
# search by rsid
get_variant(snpId = "rs1410858")

# search by variantId
get_variant(variantId = "chr1_153209640_C_A_b38")

# search by chromosome and position
get_variant(
  chromosome = "chr1",
  pos = 153209600:153209700
)
}